Some times, you want to plot the 3d-surfaces from freesurfer. Here, it is easier to use data from freesurfer (like annot and colorlut files) to create colours for the vectors. The data is somewhat more complex than the 2d ggplot polygon version ggseg ggseg3d() will create a plotly plot, which is interactive, and provides another type of flexibility to the user. A lot of credit goes to A.M.Winkler and his Brainder work, which supplied us with the first examples of going from .srf to .ply files, and whose scripts massively aided us in making this work.
The function ggseg3d(), is based in the plotly, it is recommended to get a little familiarized with with plotly.
Out-of-the-box, ggseg() works without supplying any extra information. It will create a base plot of the aparc (dkt) brain segmentations. All [...]_3d atlases have a built in colour column for default colour plotting of the segments.
The data is stored in tibbles, and looks like so:
## # A tibble: 4 x 3
## surf hemi data
## <chr> <chr> <list>
## 1 inflated left <tibble [10 × 7]>
## 2 inflated right <tibble [8 × 7]>
## 3 white left <tibble [10 × 7]>
## 4 white right <tibble [8 × 7]>
To grab all the data for a surface and hemisphere, you should reduce the data to one line, and then unnest()
## # A tibble: 8 x 9
## surf hemi atlas roi annot label mesh area colour
## <chr> <chr> <chr> <chr> <chr> <chr> <list> <chr> <chr>
## 1 infla… right yeo7_… 0001 FreeSurfer… rh_FreeSurf… <list… <NA> <NA>
## 2 infla… right yeo7_… 0002 7Networks_1 rh_7Network… <list… visual #a153…
## 3 infla… right yeo7_… 0003 7Networks_2 rh_7Network… <list… somato… #6fab…
## 4 infla… right yeo7_… 0004 7Networks_3 rh_7Network… <list… dorsal… #2c8b…
## 5 infla… right yeo7_… 0005 7Networks_4 rh_7Network… <list… ventra… #b77f…
## 6 infla… right yeo7_… 0006 7Networks_5 rh_7Network… <list… limbic #e7ed…
## 7 infla… right yeo7_… 0007 7Networks_6 rh_7Network… <list… fronto… #edaf…
## 8 infla… right yeo7_… 0008 7Networks_7 rh_7Network… <list… default #e272…
Particularly notice the mesh column, which is a list column of lists. In there is all the 6 vectors needed to create the mesh of the tri-surface plot. You’ll also need to notive the label, annot and area columns, which are likely the columns you will be matching on when proviging with your own data for colours. You need to be meticulous when fixing your data, be sure it matches. The function should give you a warning if it’s struggling to match something.
The column you want to use for colour, needs to be supplied to the colour option, and you’ll likely want to supply it to the text option, as this will add another line to the plotly hover information.
You can also change the palette. Choose from ALL the paletteer palettes, just use their name.
You can also provide custom colour palettes either in hex or R-names
ggseg3d(data = someData, atlas = yeo7_3d,
colour = "p", text = "p",
palette = c("forestgreen", "white", "firebrick")) ggseg3d(data = someData, atlas = yeo7_3d,
colour = "p", text = "p", palette = c("#ff0000", "#00ff00", "#0000ff"))If you want to alter the colour of NA regions, supply na.colour
You can rotate away all you like. if you want to start from the medial view, you can use the camera option
There is also a surface of the white-matter